biogems.info - gems for bioinformatics

New: CloudBioLinux packages are now listed on biogems.info !

#	biogem	description	by	version	released	stars	issues	total	7d	90d**)
								downloads	commits
1	bio	Bioinformatics library	BioRuby project	1.5.1	3 weeks	298	10	123728	0	0
2	biodiversity	Parser of scientific names	Dmitry Mozzherin	3.4.1	13 months	23	3	71995	0	0
3	bio samtools	Binder of samtools for Ruby, on the top	Ricardo Ramirez-Gonzalez, Dan MacLean, Raoul J.P. Bonnal	2.4.0	4 months	23	6	53705	0	0
4	bio gem	Biogem is a software generator for Ruby in	Raoul J.P. Bonnal, Pjotr Prins	1.3.6	2 years	15	12	50138	0	0
5	sequenceserver	Blast search made easy!	Anurag Priyam, Ben J Woodcroft, Vivek Rai et al.	1.0.8	6 months	103	51	41394	0	121
6	bio gadget	Gadgets for bioinformatics	Shintaro Katayama	0.4.8	3 years		1	36073	0	0
7	bio ucsc api	The Ruby ucsc api: accessing the ucsc genome	Hiroyuki Mishima, Jan Aerts	0.6.2	2 years	16	1	33949	0	0
8	entrez	Http requests to entrez e-utilities	Jared Ning	0.5.8.2	17 months	7	1	31506	0	0
9	bio svgenes	Create pretty svg-format images of features, gene models	Dan MacLean	0.4.1	2 years	11	5	29246	0	0
10	biomart	A Ruby api for interacting with biomart services	Darren Oakley	0.2.3	5 years	18	5	28522	0	0
11	bio maf	Maf parser for BioRuby	Clayton Wheeler	1.0.1	4 years	10	36	24871	0	0
12	bio gff3	Gff3 parser for big data	Pjotr Prins	0.9.1	4 years	6	2	23996	0	0
13	bio blastxmlparser	Very fast parallel blast xml to rdf/html/json/yaml/csv transformer	Pjotr Prins	2.0.4	17 months	12	1	22502	0	0
14	bio grid	A biogem to submit jobs on a queue	Francesco Strozzi	0.3.3	3 years	5	...	21951	0	0
15	search biomodel	Interfaces with biomodel search engine	Niall Beard	2.1.6	4 years	1	...	21512	0	0
16	bio polyploid tools	Tool to work with polyploids, ngs and molecular	Ricardo H. Ramirez-Gonzalez	0.7.3	13 months	1	1	19697	0	0
17	bio logger	Log4r wrapper with extra features for roles and	Pjotr Prins	1.0.1	4 years	4	2	19486	0	0
18	obo parser	A simple obo file handler	mjy	0.3.7	5 years	5	...	18433	0	0
19	biointerchange	An open source framework for transforming heterogeneous data	Joachim Baran, Kevin B. Cohen, Geraint Duck et al.	1.0.8	21 months	12	3	18347	0	0
20	bio table	Swiss army knife of tabulated data; transforming/filtering tab/csv	Pjotr Prins	1.0.0	2 years	9	20	15892	0	0
21	bio band	Data mining algorithms for jRuby	arrigonialberto86	0.1.11	3 years	15	3	15364	0	0
22	bio alignment	Support for multiple sequence alignments (msa)	Pjotr Prins	0.0.8	2 years	8	5	15232	0	0
23	bio faster	A fast parser for fastq files	Francesco Strozzi	0.4.5	4 years	10	...	15203	0	0
24	bio dbla classifier	A tool to classify and manipulate pfemp1 dbl-alpha	George Githinji	0.7.1	3 years			12757	0	0
25	bio bigbio	Low memory sequence emitters	Pjotr Prins	0.1.6	2 years	11	1	12281	0	0
26	bio phyta	Pipeline to remove contaminations from est libraries	Philipp Comans	0.9.4	4 years	2	1	12116	0	0
27	bio signalp	A wrapper for the signal peptide prediction algorith	Ben J Woodcroft	0.3.1	2 years	3	...	11758	0	0
28	nexus parser	A nexus file format (phylogenetic inference) parser in	mjy	1.1.4	5 years	1	...	11468	0	0
29	scaffolder	Build genome output files	Michael Barton	0.5.0	3 years	7	...	11320	0	0
30	bio vcf	Fast multi-purpose multi-threaded vcf parser	Pjotr Prins	0.9.2	8 months	34	8	11091	0	0
31	bio kmer counter	A biogem for counting small kmers for fingerprinting	Ben J Woodcroft	0.1.2	3 years	5	...	10954	0	0
32	bio ngs	Bio-ngs provides a framework for handling ngs data	Francesco Strozzi, Raoul J.P. Bonnal	0.5.2	4 years	30	15	10723	0	0
33	bio tm hmm	A BioRuby plugin for interaction with the transmembrane	Ben J. Woodcroft	0.2.2	3 years	2	...	10620	0	0
34	rubyMorphbank	Simple morphbank (http://morphbank.net) services accessor	mjy	0.2.6	5 years	1	...	10404	0	0
35	bio assembly	BioRuby assembly plugin	Chase Miller, Francesco Strozzi	0.1.0	5 years	4	...	10366	0	0
36	bio sambamba	Ruby wrapper for sambamba tool	Artem Tarasov	0.0.5	4 years	2	...	10299	0	0
37	eutils	Lightweight Ruby api for ncbi eutils	Joon Lee, aka seouri	0.2.1	3 years	8	...	10030	0	0
38	bio isoelectric point	A BioRuby plugin for calculating the isoelectric point	George Githinji, Pascal Betz	0.1.3	4 years	3	...	9838	0	0
39	bio rocker	Rocker	Luis (Coto) Orellana, Luis M. Rodriguez-R	1.1.12	4 months			9829	0	0
40	bio nexml	BioRuby plugin for reading and writing nexml (http://nexml.org)	Rutger Vos, Anurag Priyam	1.1.0	4 years	8	2	9816	0	0
41	bioportal	Supports linking of models within a ror application	Stuart Owen, Quyen Nguyen	2.2	2 years		...	9509	0	0
42	bio basespace sdk	Basespace Ruby sdk is a Ruby based software	Joachim Baran, Raoul Bonnal, Eri Kibukawa et al.	0.1.7	3 years	13	2	9439	0	0
43	bio graphics	Library for visualizing genomic regions	Jan Aerts	1.4	8 years	21	1	8733	0	0
44	bio genomic interval	A BioRuby plugin: handling genomic interavals and overlaps	Hiroyuki Mishima	0.1.2	5 years	4	...	8684	0	1
45	bio velvet	Parser to work with file formats used in	Ben J Woodcroft	0.6.0	20 months		...	8611	0	0
46	bio bgzf	Reading/writing bgzf blocks	Artem Tarasov, Clayton Wheeler	0.2.1	4 years	3	...	8504	0	0
47	bio polymarker db batch	Server for polymarker. to be used with cron	Ricardo H. Ramirez-Gonzalez	0.5.1	19 months		...	8413	0	0
48	bio octopus	Running and parsing of the protein transmembrane domain	Ben J Woodcroft	0.1.1	5 years	1	...	7948	0	0
49	bio cd hit report	Read and manipulate cd-hit clusters	George Githinji	0.1.0	3 years			7346	0	0
50	bio bwa	Ruby binding for bwa mapping software	Francesco Strozzi	0.2.2	5 years	4	...	7291	0	0
51	bio tabix	Ruby binding for samtools tabix	throwern	1.0.1	2 years	5	...	7181	0	0
52	bio lazyblastxml	A plugin that allows you to parse large	robsyme	0.4.0	5 years	1	...	7043	0	0
53	bio pileup iterator	Iterate through a samtools pileup file	Ben J. Woodcroft	0.0.4	3 years	2	...	6838	0	0
54	goruby	Gene ontology (go) interface for Ruby	Ben J Woodcroft	0.2.0	5 years	10	...	6815	0	0
55	genevalidator	Identifying problems with gene predictions	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	1.6.12	4 months	1	...	6781	0	0
56	taxonifi	A general purpose framework for scripted handling of development/stable	mjy	0.4.0	3 years	2	1	6532	0	0
57	ruby ensembl api	Api to ensembl databases	Jan Aerts, Francesco Strozzi	1.0.1	5 years	41	5	6328	0	0
58	bio gff3 pltools	Ruby wrapper for the gff3-pltools	Marjan Povolni	0.3.0	4 years	13	19	6096	0	0
59	bio fasta retrieve	Retrieve dna sequence from ucsc using given coordinates	Andrei Rozanski	0.0.7	13 months			6086	0	0
60	bio plasmoap	Implementation of the plasmoap algorithm	Ben J Woodcroft	0.1.1	5 months	1	...	6033	0	0
61	bio chembl	Chembl rest api client, parser and container	Mitsuteru Nakao	0.1.3	4 years	1	1	5988	0	0
62	bio gngm	Next-generation mapping of mutations	Dan MacLean	0.2.1	3 years	2	...	5987	0	0
63	bio ucsc util	Ruby binding to the ucsc kent utilities	throwern	0.1.2	3 years	2	...	5913	0	0
64	bio statsample timeseries	Timeseries modules for statsample	Ankur Goel, Claudio Bustos	0.2.1	3 years			5822	0	0
65	publisci	Publish scientific results to the semantic web	Will Strinz	0.1.6	2 years	3	16	5630	0	0
66	bio krona	This biogem is built around krona, a flashy	Ben J. Woodcroft	0.2.0	9 months	1	...	5554	0	0
67	bio rdf	Bioinformatics triple-store support	Pjotr Prins	0.0.2	4 years	4	1	5510	0	0
68	bio affy	Parse affymetrix cel/cdf files	Pjotr Prins	0.5.1	4 years	2	1	5484	0	0
69	bio fastqc	Ruby parser for fastqc output	Tazro Inutano Ohta	0.8.0	11 weeks	2	...	5452	0	13
70	bio kb illumina	Geneexpression illuminahumanannotation	Raoul J.P. Bonnal	0.1.0	5 years	1	...	5427	0	0
71	bio velvet underground	Bindings to some internals of the velvet assembler	Ben Woodcroft	0.3.1	8 weeks		1	5401	0	0
72	bio unichem	BioRuby plugin for unichem rest web service	Mitsuteru Nakao	0.3.0	3 years			5142	0	0
73	bio synreport	Reports whether a nucleotide change results in synonymous	Dan MacLean	0.1.2	3 years		...	5043	0	0
74	bio core	BioRuby core plugins, most and stable plugins. blastxmlparser,	Raoul J.P. Bonnal	0.0.1	5 years	1	...	4820	0	0
75	bio liftover	Ruby solution for ucsc liftover tool- (ucsc http://genome.ucsc.edu/cgi-bin/hgliftover)	Andrei Rozanski	1.3.0	2 years	1	...	4660	0	0
76	bio cnls screenscraper	Programmatic interface to the cnls nuclear localisation signal	Ben J. Woodcroft	0.3.0	4 years	2	...	4636	0	0
77	bio wolf psort wrapper	Enables the localisation predictor wolf psort to be	Ben J Woodcroft	0.0.3	4 years	1	...	4630	0	0
78	bio commandeer	Dead simple method of running shell commands from	Ben J. Woodcroft	0.1.3	5 months		...	4364	0	0
79	bio hmmer model	Parse pfam hmm definition files	Ben J. Woodcroft	0.0.2	4 years	1	...	4229	0	0
80	bio protparam	A protparam compatible utility for BioRuby	hryk	0.2.0	3 years	2	...	4211	0	0
81	genevalidatorapp	A web app wrapper for genevalidator	Monica Dragan, Ismail Moghul, Anurag Priyam et al.	1.5.4	2 weeks	1	...	4076	0	0
82	bio gag	Bio-gag is a biogem for detecting and correcting	Ben J Woodcroft	0.1.0	3 years	2	...	4063	0	0
83	ref2bibtex	Pass a full citation, get the bibtex back,	Matt Yoder	0.0.3	23 months		1	3535	0	0
84	bio biostars analytics	Biostars data-mining and statistical analysis	Joachim Baran	0.2.0	2 years			3527	0	0
85	bio pipengine	A pipeline manager	Francesco Strozzi, Raoul Jean Pierre Bonnal	0.9.3	4 months	14	6	3421	0	0
86	bio hmmer3 report	Enables parsing of hmmer version 3 reports	Christian Zmasek, Ben J Woodcroft	0.1.0	13 months	2	1	3299	0	0
87	nbio cloudquery	Client for xoopit's cloudquery api	Cameron Walters, nb.io	0.1.5	7 years	5	...	3172	0	0
88	bio gggenome	Gggenome Ruby client	Mitsuteru Nakao	0.2.0	3 years	1	...	3129	0	0
89	bio locus	Fast storage and comparison of chr+pos(+alt) locations	Pjotr Prins	0.0.7	12 months	2	1	3103	0	0
90	bio ensembl rest	Ruby ensembl rest api	Alberto Donizetti	0.2.0	3 years	3	...	3074	0	0
91	rubyBHL	Rubybhl is a simple request/response wrapper for the	Matt Yoder	0.2.1	2 years	6	...	3008	0	0
92	bio statsample glm	Generalized linear models for statsample	Ankur Goel	0.1.1	3 years			2942	0	0
93	bio hello	Hello world plugin for the BioRuby (just for	Toshiaki Katayama	0.0.0	5 years	3	...	2850	0	0
94	bio sge	BioRuby plugin for sun grid engine	Toshiaki Katayama	0.0.0	5 years	4	...	2837	0	0
95	bio sra	A sequence read archive (sra) download script and	Ben J. Woodcroft	0.3.1	9 months	2	...	2836	0	0
96	bio restriction enzyme	Digests dna based on restriction enzyme cut patterns	Trevor Wennblom	1.0.0	5 years		1	2798	0	0
97	bio express beta diversity	Interface for express beta diversity	Ben J. Woodcroft	0.1.0	2 years		...	2749	0	0
98	dna sequence aligner	Does high pairwise alignment of sequencing reads with	John T. Prince	0.0.2	6 years	1	...	2729	0	0
99	bio repeatmasker	Bio-repeatmasker	Andrei Rozanski	0.0.3	2 years		...	2684	0	0
100	bio emboss six frame nucleotide sequences	A method to get the nucleotide sequence of	Ben J Woodcroft	0.1.0	5 years	1	...	2623	0	0
101	bio core ext	BioRuby core ext: plugins which require external library	Raoul J.P. Bonnal, Pjotr Prins	0.0.1	5 years	1	...	2556	0	0
102	bio biolinux	Meta package for biolinux distribution	Raoul J.P. Bonnal	0.1.0	5 years	2	...	2547	0	0
103	bio ensembl	A Ruby api to the ensembl database	Jan Aerts, Francesco Strozzi	1.1.0	4 years	4	...	2533	0	0
104	bio cigar	A parser for cigar format alignments	Ben J Woodcroft	0.1.0	2 years	4	...	2526	0	0
105	bio data restriction enzyme	Restriction enzyme dataset	Sir Richard J. Roberts, Trevor Wennblom	1.109.0	5 years		...	2514	0	0
106	bio foo	One-line summary of your gem	Toshiaki Katayama	0.0.0	4 years	1	...	2513	0	0
107	intermine bio	Biological extensions for the intermine webservice client library	Alex Kalderimis	0.98.1	5 years	1	...	2480	0	0
108	bio dbsnp	Decoding the dbsnp bitfield	Hiroyuki Mishima	0.1.1	4 years	4	...	2474	0	0
109	bio phyloxml	Phyloxml plugin for BioRuby	Diana Jaunzeikare, Clayton Wheeler	0.9.0	4 years	3	1	2459	0	0
110	bio exportpred	Wrapper around the exportpred algorithm for predicting p	Ben J Woodcroft	0.0.1	4 years	1	...	2457	0	0
111	bio hydropathy	Hydropathy scale for BioRuby	Ben J Woodcroft	0.0.1	4 years	1	...	2457	0	0
112	bio samtools server	Web server for bio-samtools	homonecloco	0.1.2	2 years		...	2451	0	0
113	bio aliphatic index	A simple biogem that allows computation of the	Ben J Woodcroft	0.0.1	4 years	1	...	2427	0	0
114	bio mummer	Helper methods for reading .delta files	robsyme	0.2.1	18 months		...	2411	0	0
115	bio ipcress	A programmatic interface to the ipcress in-silico pcr	Ben J Woodcroft	0.0.1	4 years	3	...	2337	0	0
116	bio incanter	Build graph with jRuby	Matteo Picciolini	0.1.0	4 years			2254	0	0
117	nbio csshttprequest	Csshttprequest is cross-domain ajax using css as a	Cameron Walters, Randy Reddig	1.0.3	7 years	89	1	2245	0	0
118	ncbi blast dbs	Fast download blast databases from ncbi beta	Anurag Priyam	0.0.5	7 months	4	1	2196	0	0
119	bio img metadata	Reads metadata from integrated microbial genomes (img) metadata	Ben J. Woodcroft	0.0.1	3 years		...	2006	0	0
120	bio stockholm	Parse stockholm sequence alignment format	Ben J. Woodcroft	0.0.1	3 years	2	...	1823	0	0
121	bio raxml	Ruby wrapper to run standard-raxml for maximum likelihood	Fernando Izquierdo	0.1.0	3 years		...	1738	0	0
122	bio gfastqc	Aggregate fastqc (quality control for next generation sequencing	Raoul Jean Pierre Bonnal	0.0.4	15 months		...	1592	0	0
123	bio freebayes	The api for freebayes version #{bio::freebayes::extversion}	Natapol Pornputtapong	0.1.6	16 months			1532	0	0
124	bio old biofetch emulator	Emulates as if old BioRuby biofetch alives	Naohisa Goto	1.0.0	3 months		...	1485	0	0
125	bio kseq	Ruby inferface for kseq.h by heng li for	Fedor Gusev	0.0.2	2 years	2	...	1384	0	0
126	bio exominer	Mine publications for gene names	Pjotr Prins	0.0.3	2 years		...	1356	0	0
127	bark	A Ruby wrapper on the open tree api beta	Matt Yoder	0.0.2	2 years	1	...	1256	0	0
128	genomichdt	A restful service for sharing genomic data	Joachim Baran, Robert Buels, Michel Dumontier	0.0.1	2 years			1244	0	0
129	bio faidx	Tools to work with fasta files, indexed with	homonecloco	0.0.1	24 months		...	1194	0	0
130	bio blat tools	Tools to manipulate blat files from the command	homonecloco	0.1.0	24 months		...	1162	0	0
131	bio location rdfize	Faldo location output method for bio::location in BioRuby	Joachim Baran, Naohisa Goto	0.0.0	22 months		...	1132	0	0
132	bio picard	Api of picard tool	Natapol Pornputtapong	1.131.5	16 months			1035	0	0
133	nbio css http request	Csshttprequest is cross-domain ajax using css disabled	Cameron Walters, Randy Reddig	0.1	7 years			996	0	0
134	bio conduit	A pipeline creator for BioRuby	Natapol Pornputtapong	1.0.0	13 months			751	0	0
135	bio jaspar	Tools for jaspar motifs in BioRuby	Jessica Lee, Wasserman Lab	0.1.0	12 months		...	738	0	0
136	bio kallisto	Basic wrapper for the kallistio mapper	homonecloco	0.1.0	11 months	1	...	719	0	0
137	bio sparql client	A Ruby wrapper for bio sparql service	Natapol Pornputtapong	0.0.1	17 months			697	0	0
138	bio plates	Methods for handling multiwell plate annotations	Steve Pettitt	0.2.0	8 months		...	563	0	0
139	bio sam mutation	Parsing and mutation calling from sam, cigar and	Stephen Pettitt	0.4.1	7 months		...	506	0	0
140	bio biosql	Biosql plugin for BioRuby	BioRuby project	0.0.0	3 months		...	262	0	0
141	bio primer3	pre		pre			...	0	0	0

*) gem downloads (total & last 90 days) from rubygems.org as of 2016-09-28
**) number of commits on GitHub (last 7 days & last 90 days)